| Next changeset 1:2c1cb37a3ffe (2019-05-08) |
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Commit message:
planemo upload commit 80c22275be05e29208e991019309dfffa9704f39 |
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added:
contains.xml matches.xml test-data/SRR1203042_1-head4000-contains.tab test-data/SRR1203042_1-head4000-refseq_masher-matches-m2.tab test-data/SRR1203042_1-head4000.fastq test-data/Se-Enteritidis-refseq_masher-matches.tab test-data/Se-Enteritidis.fasta |
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| diff -r 000000000000 -r 26df66c32861 contains.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/contains.xml Thu Feb 15 13:59:31 2018 -0500 |
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| b'@@ -0,0 +1,323 @@\n+<tool id="refseq_masher_contains" name="RefSeq Masher Contains" version="0.1.1">\n+ <description>\n+ Find NCBI RefSeq Genomes contained in your sequences\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="0.1.1">refseq_masher</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+<![CDATA[\n+\n+#import re\n+\n+#if $input.type == \'fasta\'\n+#set $input_files = \'"{}"\'.format($input.fasta.name)\n+ ln -s "$input.fasta" $input_files &&\n+#elif $input.type == \'paired\'\n+#set $_forward_ext = \'.fastq.gz\' if $re.match(r\'.*\\.gz$\', $input.forward.name) else \'.fastq\'\n+#set $_forward = \'"{}_1{}"\'.format($re.sub(r\'_[12]\\..+$\', \'\', $input.forward.name), $_forward_ext)\n+#set $_reverse_ext = \'.fastq.gz\' if $re.match(r\'.*\\.gz$\', $input.reverse.name) else \'.fastq\'\n+#set $_reverse = \'"{}_2{}"\'.format($re.sub(r\'_[12]\\..+$\', \'\', $input.reverse.name), $_reverse_ext)\n+#set $input_files = \'{} {}\'.format($_forward, $_reverse)\n+ ln -s "$input.forward" $_forward &&\n+ ln -s "$input.reverse" $_reverse &&\n+#elif $input.type == \'single\'\n+#set $input_files = \'"{}"\'.format($input.single.name)\n+ ln -s "$input.single" $input_files &&\n+#elif $input.type == \'paired_collection\'\n+#set $_forward_ext = \'.fastq.gz\' if $re.match(r\'.*\\.gz$\', str($input.paired_collection.forward)) else \'.fastq\'\n+#set $_forward = \'"{}_1{}"\'.format($input.paired_collection.name, $_forward_ext)\n+#set $_reverse_ext = \'.fastq.gz\' if $re.match(r\'.*\\.gz$\', str($input.paired_collection.reverse)) else \'.fastq\'\n+#set $_reverse = \'"{}_2{}"\'.format($input.paired_collection.name, $_reverse_ext)\n+#set $input_files = \'{} {}\'.format($_forward, $_reverse)\n+ ln -s "$input.paired_collection.forward" $_forward &&\n+ ln -s "$input.paired_collection.reverse" $_reverse &&\n+#end if\n+\n+refseq_masher\n+ $adv.verbosity\n+ contains\n+ --output refseq_masher-contains.${adv.output_type}\n+ --output-type $adv.output_type\n+ --top-n-results $adv.top_n_results\n+ --parallelism "\\${GALAXY_SLOTS:-1}"\n+ --min-identity $adv.min_identity\n+ --max-pvalue $adv.max_pvalue\n+ $input_files\n+\n+]]>\n+ </command>\n+ <inputs>\n+ <conditional name="input">\n+ <param name="type" type="select" label="Sequence input type">\n+ <option value="fasta">FASTA</option>\n+ <option value="paired">Paired-end FASTQs</option>\n+ <option value="single">Single-end FASTQ</option>\n+ <option value="paired_collection">Paired-end FASTQ collection</option>\n+ </param>\n+ <when value="fasta">\n+ <param name="fasta"\n+ type="data" format="fasta"\n+ optional="false"\n+ label="FASTA file"\n+ />\n+ </when>\n+ <when value="paired">\n+ <param name="forward"\n+ type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"\n+ optional="false"\n+ label="Forward FASTQ file"\n+ help="Must have ASCII encoded quality scores"\n+ />\n+ <param name="reverse"\n+ type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"\n+ optional="false"\n+ label="Reverse FASTQ file"\n+ help="File format must match the Forward FASTQ file"\n+ />\n+ </when>\n+ <when value="single">\n+ <param name="single"\n+ type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"\n+ optional="false"\n+ label="Single-end FASTQ file"\n+ />\n+ </when>\n+ <when value="paired_collection">\n+ <param name="paired_collection"\n+ type="data_collection" format="fastq,fastqsanger,fastqillumina,fastqsolexa,fastq.gz,txt"\n+ collection_type="paired"\n+ optional="false"\n+ label="Paired-end FASTQ collection"\n+ help=""\n+ />\n+ </when>\n+ </conditional>\n+ <section name="adv" title="Advanced Options" expanded="false">\n+ <param name="top_n_results"\n+ type="integer"\n+ label="Top N matches to report (0 to report all)"\n+ min="0"\n+ '..b' | pMRC151 | | | 573 | | ./rcn/refseq-NG-573-.-.-.-pMRC151-Klebsiella_pneumoniae.fna | | |\n++-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+\n+| [37 rows] | | | | | | | | | | | | | | | | | | | | | | | | |\n++-----------+--------------------------------------+----------+----------------+----------------------+--------+--------------------------------------------------------------------------------------------------------------------------------------------------+-----------------------+------------------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+---------+----------+------------+-----------+---------+---------------------+----------------------------------------------------------------------------------------------+--------------------------+----------------+\n+\n+Some of the top genomes contained in this sample are sorted by identity and median multiplicity are:\n+\n+- *Bacteroides fragilis* - fully contained (400/400) and high multiplicity (768)\n+- *Escherichia coli* O104:H4 - fully contained (400/400) and median multiplicity of 48\n+- *Kingella kingae* - fully contained (400/400) and median multiplicity of 5\n+- *Klebsiella pneumoniae* - 399/400 sketches contained with median multiplicity of 4\n+\n+So with Mash we are able to find that the sample contained the expected genomic data (especially *E. coli* O104:H4). \n+\n+\n+\n+Legal\n+-----\n+\n+Copyright Government of Canada 2017\n+\n+Written by: National Microbiology Laboratory, Public Health Agency of Canada\n+\n+Licensed under the Apache License, Version 2.0 (the "License"); you may not use\n+this work except in compliance with the License. You may obtain a copy of the\n+License at:\n+\n+http://www.apache.org/licenses/LICENSE-2.0\n+\n+Unless required by applicable law or agreed to in writing, software distributed\n+under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR\n+CONDITIONS OF ANY KIND, either express or implied. See the License for the\n+specific language governing permissions and limitations under the License.\n+\n+Contact\n+-------\n+\n+**Gary van Domselaar**: gary.vandomselaar@phac-aspc.gc.ca\n+\n+\n+\n+.. _Mash: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x\n+.. _SAMEA1877340: https://www.ebi.ac.uk/ena/data/view/SAMEA1877340\n+.. _PRJEB1775: https://www.ebi.ac.uk/ena/data/view/PRJEB1775\n+.. _ERR260489: https://www.ebi.ac.uk/ena/data/view/ERR260489&display=html\n+\n+]]>\n+ </help>\n+ <citations>\n+ <!-- Citation for Mash paper -->\n+ <citation type="doi">10.1186/s13059-016-0997-x</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 26df66c32861 matches.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/matches.xml Thu Feb 15 13:59:31 2018 -0500 |
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| b'@@ -0,0 +1,294 @@\n+<tool id="refseq_masher_matches" name="RefSeq Masher Matches" version="0.1.1">\n+ <description>\n+ Find closest matching NCBI RefSeq Genomes to your sequences\n+ </description>\n+ <requirements>\n+ <requirement type="package" version="0.1.1">refseq_masher</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code">\n+<![CDATA[\n+\n+#import re\n+\n+#if $input.type == \'fasta\'\n+#set $input_files = \'"{}"\'.format($input.fasta.name)\n+ ln -s "$input.fasta" $input_files &&\n+#elif $input.type == \'paired\'\n+#set $_forward_ext = \'.fastq.gz\' if $re.match(r\'.*\\.gz$\', $input.forward.name) else \'.fastq\'\n+#set $_forward = \'"{}_1{}"\'.format($re.sub(r\'_[12]\\..+$\', \'\', $input.forward.name), $_forward_ext)\n+#set $_reverse_ext = \'.fastq.gz\' if $re.match(r\'.*\\.gz$\', $input.reverse.name) else \'.fastq\'\n+#set $_reverse = \'"{}_2{}"\'.format($re.sub(r\'_[12]\\..+$\', \'\', $input.reverse.name), $_reverse_ext)\n+#set $input_files = \'{} {}\'.format($_forward, $_reverse)\n+ ln -s "$input.forward" $_forward &&\n+ ln -s "$input.reverse" $_reverse &&\n+#elif $input.type == \'single\'\n+#set $input_files = \'"{}"\'.format($input.single.name)\n+ ln -s "$input.single" $input_files &&\n+#elif $input.type == \'paired_collection\'\n+#set $_forward_ext = \'.fastq.gz\' if $re.match(r\'.*\\.gz$\', str($input.paired_collection.forward)) else \'.fastq\'\n+#set $_forward = \'"{}_1{}"\'.format($input.paired_collection.name, $_forward_ext)\n+#set $_reverse_ext = \'.fastq.gz\' if $re.match(r\'.*\\.gz$\', str($input.paired_collection.reverse)) else \'.fastq\'\n+#set $_reverse = \'"{}_2{}"\'.format($input.paired_collection.name, $_reverse_ext)\n+#set $input_files = \'{} {}\'.format($_forward, $_reverse)\n+ ln -s "$input.paired_collection.forward" $_forward &&\n+ ln -s "$input.paired_collection.reverse" $_reverse &&\n+#end if\n+\n+refseq_masher \n+ $adv.verbosity \n+ matches \n+ --output refseq_masher-matches.${adv.output_type}\n+ --output-type $adv.output_type\n+ --top-n-results $top_n_results\n+#if $adv.min_kmer_threshold\n+ --min-kmer-threshold $adv.min_kmer_threshold\n+#end if\n+ -T "\\${TMPDIR:-/tmp}"\n+ $input_files\n+]]>\n+ </command>\n+ <inputs>\n+ <conditional name="input">\n+ <param name="type" type="select" label="Sequence input type">\n+ <option value="fasta">Genome FASTA</option>\n+ <option value="paired">Paired-end FASTQs</option>\n+ <option value="single">Single-end FASTQ</option>\n+ <option value="paired_collection">Paired-end FASTQ collection</option>\n+ </param>\n+ <when value="fasta">\n+ <param name="fasta"\n+ type="data" format="fasta"\n+ optional="false"\n+ label="Genome FASTA file"\n+ />\n+ </when>\n+ <when value="paired">\n+ <param name="forward"\n+ type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"\n+ optional="false"\n+ label="Forward FASTQ file"\n+ />\n+ <param name="reverse"\n+ type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"\n+ optional="false"\n+ label="Reverse FASTQ file"\n+ help="File format must match the Forward FASTQ file"\n+ />\n+ </when>\n+ <when value="single">\n+ <param name="single"\n+ type="data" format="fastq,fastqsanger,fastqillumina,fastqsolexa"\n+ optional="false"\n+ label="Single-end FASTQ file"\n+ />\n+ </when>\n+ <when value="paired_collection">\n+ <param name="paired_collection"\n+ type="data_collection" format="fastq,fastqsanger,fastqillumina,fastqsolexa,fastq.gz,txt"\n+ collection_type="paired"\n+ optional="false"\n+ label="Paired-end FASTQ collection"\n+ />\n+ </when>\n+ </conditional>\n+ <param name="top_n_results"\n+ type="integer"\n+ min="0"\n+ value="20"\n+ optional="true"\n+ label="Top N matches to report (set to 0 to report all)"\n+ />\n+ <section name="adv" title="Advanced Options" expanded="false">\n+ <param'..b'mily | taxonomic_order | taxonomic_class | taxonomic_phylum | taxonomic_superkingdom | subspecies | serovar | plasmid | bioproject | biosample | taxid | assembly_accession | match_id |\n++=======================================+====================================================================+==========+========+==========+=============================================================================================================================================================+=====================================+=====================+==================+====================+==================+=====================+===================+=========================+============+=============+=========+=============+==============+========+=====================+==========================================================================================================================================+\n+| GCF_000329025.1_ASM32902v1_genomic | Salmonella enterica subsp. enterica serovar Enteritidis str. CHS44 | 0.0 | 0.0 | 400/400 | Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Enteritidis; str. CHS44 | Salmonella enterica subsp. enterica | Salmonella enterica | Salmonella | Enterobacteriaceae | Enterobacterales | Gammaproteobacteria | Proteobacteria | Bacteria | enterica | Enteritidis | | PRJNA185053 | SAMN01041154 | 702979 | NZ_ALFF | ./rcn/refseq-NZ-702979-PRJNA185053-SAMN01041154-NZ_ALFF-.-Salmonella_enterica_subsp._enterica_serovar_Enteritidis_str._CHS44.fna |\n++---------------------------------------+--------------------------------------------------------------------+----------+--------+----------+-------------------------------------------------------------------------------------------------------------------------------------------------------------+-------------------------------------+---------------------+------------------+--------------------+------------------+---------------------+-------------------+-------------------------+------------+-------------+---------+-------------+--------------+--------+---------------------+------------------------------------------------------------------------------------------------------------------------------------------+\n+\n+\n+The top match is *Salmonella enterica* subsp. enterica serovar Enteritidis str. CHS44_ with a distance of 0.0 and 400/400 sketches matching, which is what we expected. There\'s other taxonomic information available in the results table that may be useful. \n+\n+\n+\n+Legal\n+-----\n+\n+Copyright Government of Canada 2017\n+\n+Written by: National Microbiology Laboratory, Public Health Agency of Canada\n+\n+Licensed under the Apache License, Version 2.0 (the "License"); you may not use\n+this work except in compliance with the License. You may obtain a copy of the\n+License at:\n+\n+http://www.apache.org/licenses/LICENSE-2.0\n+\n+Unless required by applicable law or agreed to in writing, software distributed\n+under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR\n+CONDITIONS OF ANY KIND, either express or implied. See the License for the\n+specific language governing permissions and limitations under the License.\n+\n+Contact\n+-------\n+\n+**Gary van Domselaar**: gary.vandomselaar@phac-aspc.gc.ca\n+\n+.. _Mash: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0997-x\n+.. _FNA.GZ: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/GCF_000329025.1_ASM32902v1_genomic.fna.gz\n+.. _CHS44: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/329/025/GCF_000329025.1_ASM32902v1/\n+\n+\n+]]>\n+ </help>\n+ <citations>\n+ <!-- Citation for Mash paper -->\n+ <citation type="doi">10.1186/s13059-016-0997-x</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 26df66c32861 test-data/SRR1203042_1-head4000-contains.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR1203042_1-head4000-contains.tab Thu Feb 15 13:59:31 2018 -0500 |
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| @@ -0,0 +1,6 @@ +sample top_taxonomy_name identity shared_hashes median_multiplicity pvalue full_taxonomy taxonomic_subspecies taxonomic_species taxonomic_genus taxonomic_family taxonomic_order taxonomic_class taxonomic_phylum taxonomic_superkingdom subspecies serovar plasmid bioproject biosample taxid assembly_accession match_id match_comment +SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Typhimurium 0.934797 136/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Typhimurium Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Typhimurium PRJNA188943 90371 ./rcn/refseq-NG-90371-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Typhimurium.fna +SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Typhimurium 0.934797 136/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Typhimurium Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Typhimurium PRJNA188943 90371 ./rcn/refseq-NR-90371-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Typhimurium.fna +SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Choleraesuis 0.9326110000000001 131/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Choleraesuis Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Choleraesuis PRJNA188943 119912 ./rcn/refseq-NG-119912-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Choleraesuis.fna +SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Choleraesuis 0.9326110000000001 131/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Choleraesuis Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Choleraesuis PRJNA188943 119912 ./rcn/refseq-NR-119912-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Choleraesuis.fna +SRR1203042-head4000 Atlantibacter hermannii 0.9224829999999999 110/400 1 0.0 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Atlantibacter; hermannii Atlantibacter hermannii Atlantibacter Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria PRJNA33175 565 ./rcn/refseq-NR-565-PRJNA33175-.-.-.-Escherichia_hermannii.fna |
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| diff -r 000000000000 -r 26df66c32861 test-data/SRR1203042_1-head4000-refseq_masher-matches-m2.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR1203042_1-head4000-refseq_masher-matches-m2.tab Thu Feb 15 13:59:31 2018 -0500 |
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| @@ -0,0 +1,2 @@ +sample top_taxonomy_name distance pvalue matching full_taxonomy taxonomic_subspecies taxonomic_species taxonomic_genus taxonomic_family taxonomic_order taxonomic_class taxonomic_phylum taxonomic_superkingdom subspecies serovar plasmid bioproject biosample taxid assembly_accession match_id +SRR1203042-head4000 Salmonella enterica subsp. enterica serovar Typhimurium 0.141301 7.688639999999999e-108 22/400 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Typhimurium Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Typhimurium PRJNA188943 90371 ./rcn/refseq-NR-90371-PRJNA188943-.-.-.-Salmonella_enterica_subsp._enterica_serovar_Typhimurium.fna |
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| diff -r 000000000000 -r 26df66c32861 test-data/SRR1203042_1-head4000.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/SRR1203042_1-head4000.fastq Thu Feb 15 13:59:31 2018 -0500 |
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| b'@@ -0,0 +1,4000 @@\n+@SRR1203042.1 1/1\n+GCCCAGTGCAGTGCCTCACGATCNCAGCAGTCCAGCGCGAACGTGACGCGCAGTTTTTCTCCGTTATCACAGCGGAACTCGAACCCGTCAGAGCACCATCGC\n++\n+BBBBBBFFFFFFGGGGGFGGCGH#AAFF2EGHHHHHGGC2AEGGHHGGGGGGGGHHHGHHHHGHHGHHHHHHHGGGGGHHCHHHGGGGGGGHHHHHHHHHGG\n+@SRR1203042.2 2/1\n+CCCTTCGCCAATGCCCTGCGATGCGCCCGTAATCAATGCTGTCTTGCCCGTGAGTTTACCCATTTTCAATGTCTCCTTTTGAATATGGAGTCTTACACTCCATTAACACTGAAAATACAGTAATAACAAATAAGTGCTGAGGAATAGCTCACTAATTCAGGTAAATATTAGGTAAAAAAATCCCCGCGGAGGCGGGGATGGGCATTTTTATGCTGTTCTGCCTGATGGCGCTGCGCTTATCAGGCCTACCA\n++\n+CCCCCFCCCCCFGGGGGGGGGGGGGGGGCEEFGHHHHHHHHHHHHHHHHGGGGGHGHHHHHHHHHHHHHHHHHHHHHHHHGGHHHHHGHHHHHHHHHHHHHHHHHGHFHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHGHGHHHHHGHHHHHHHHHHHHHHHEHHHHHGHHHHHHHHGGHHBGFGGGGGGGGGGGFAF?EFFFFFFFFFEFFFFFFBFBFFBBBFFFFFABADFF@D.FFFFFFFFFFF/\n+@SRR1203042.3 3/1\n+GAATTTAGTTAGCTCAAACTGTTGTGCGGAATAGTCAGGACAGAAGATTCTACCATGAGTCTGAAGGTCGCTGACACTGGCAGTCTGAGTGTTAATCAGTATGGATGGATTAACATCTGGACGGCTATTTTAGGTCACTTCTTCGCCCAATTTCCAGCTTTTTTTGAAGGCCGTCGCAATGTCGGTCAAAATCAGGCGGTAAACGTTTCTGATAATGCTGACATTATGCGCATTTATGCTTTGCTTTTTTT\n++\n+AABAAFFBDFFFGFGFGGGGGFGDBADEGGGGHFHHH52BFFA3BFFGHDGFFFFHFHCEAEBAGBGCGEEGGGHHCHEH12EBFGHBHDGGFHFHFFEB4GHG3FECBEGFGDHHHFF3BF@@?EE3GHFHF3?B1FGDGEDDCBAADGFFFHDFDGGFGGHCCCF1>G.CC-@@GGGGHHGEC:.;0:GHFCCGBB?;C.9CE9CBBFFBFB9FB;CF/BFFFFBF/99>.9BBF//BF//;BFFFF9@\n+@SRR1203042.4 4/1\n+CGTATAGCGAGAAGACCGCCAGCGCGCCGTTTTGCCCGAAGAAGGCGGCGGCAAAGACGGCGAAAATCGCCAGGCGCGCGCCACAGGACATAAACGGCGCCATCATGATGGTCATCAGGCGTTCGCGCGGAGCGTCAAGCGTGCGGGCGCCCATCACGGAAGGTACG\n++\n+BCCCCFFFCCCCGGGGGGGGGEFEFFGGGGGHGHHHHGGGGGHHHHGGGGGGGGHGHHFGCGGGGGHHGGGGGGHGGGGGGGGGHGHHHHHHHHHGGGGGGGGGGGGGGGGFFGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFAFFFFFFFFFFFFFFFFFFFF\n+@SRR1203042.5 5/1\n+CCTTTACCCCTGCGCTACACACGCTTTTTTTGCAACGCTGGCGGTTAAGTCTGGTCGTGCAGGCCACCACGTTAAACCAACAACTACTGGAAGAAGAGCGCGAGCAGTTGCTGAG\n++\n+CCCEDFFFFDEDGGGGGGGGGGGGGGGHHGGGHHHHGGGGGGGGEEAGF5FGDHDEEEFEHFHAFFFHHEEFH2FG?G/G/?G/FC3EFG3GECGC?F2B@B/<<AGDG1DGH1G\n+@SRR1203042.6 6/1\n+CTTCCAGGCCGCCATCATGAGCGGATAATTCCACGGCGCGATAGAGGCAACCACGCCAATCGGATCCCGGCGGATCATCGACGTATGTCCTTCCAGATATTCGCCCGCCGCCAGCCCACTCAAACAACGGGCCGCGCCGGCAAAAAAGCGAAAGACATCCACGATTGCCGGAATTTCATCATTAATTACGCAGTGCAAAGGC\n++\n+ABCCCFFFCCCCGGGGGGGGGGGGGGGHHHHHHHGGGGGGGGGGHHGGGHHHGGGGGGGHHGGGGGHHGGGGGGGGHHHHHGGGHHHHHHHHHHHHHHHHHHGGGGGGGDGGGGGGGHGHHHHHHHHHGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF\n+@SRR1203042.7 7/1\n+TCACAAATCCCACCTCTTCCAGAAGATTATCGTAACTTGAAGAAAGCATGACCCTCGCCCCCGGACGCACATAGCGGCAGAAGTGGCCAATACCATACCAGGAGTGGTTACGCCGCAGCACGTCGTTTTGCGCATCGTATTGAATGGGCGCTTCACACAGATTACCC\n++\n+CDCDEFFFFFFFGGGGGGGGGGHHHHHHHHHHHHHGHHHHHHHHHHHHHHHHHHHHGGGGGGGGGGGGGGGHHHHGGGGGGHHGHHGHHHHHHHHHHHHHHGHGHHGHGHHGGGGGGGGHHGHHGGGGGHHGGGGGGHHHHHHHHHHHHGGGGGGGGGGGGGGGGGG\n+@SRR1203042.8 8/1\n+TAATAAAAAAATCAGGAGAACGGGGATGAATTTTCCATTAATTGCGAACATTGCAGTGTTCGTCATTCTGCTGTTTGTACTGGCGCAGGCCCGTCATAAACAGTGGAGTCTGGCTAAAAAAGTGCTTGTCGGCCTTGTGATGGGC\n++\n+AABBBFFFFBBFGGGGFFAFBEDAFGGGCD5FHFGFBGHDEGHF5EFCFGHHHHHHHGGGHEGGGFHGHHHHHFGHHHGHHHHGGGEGFGGGFEFEHHHHHGHGGHHHGHHHGHHHHHHFGGFHHHHHHHDGGGGHHHHFHHHHH\n+@SRR1203042.9 9/1\n+AATCTTCGCCACTCAACTTTCCTCCGTGCTCATACATAAACTAAATCGAAATGTGATTAAAACATACCAGATCTTCTTTAGAAGATCTCCCAAATAAACTCATAATTGTATGTCAACCGCTTCAAATCTTAAGCTCTATTGCCTCAATAGGTTCTATTATAATTTCGAGTATTCATATGGTGTAATGGAACCGTAGCGACAAGCATCAAGATAATC\n++\n+ACCCCFFDCCCCGGGGGGGGGGHHHGHGGGHHHHHHHHHHHHHHHHHGHHGHHHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHGGGGGHHHHHHHHHHHHHHHHHHGHHHHFHHHHHHHHHHHHHHHHHHHHGHHGHHHHHHHHHHHHHHHHHHHHGGGHGGGGGGGHGGHHHHHGHHHHH\n+@SRR1203042.10 10/1\n+GTTGTGTAGTAATTGAATACTGTAGAAACACTTCATTCATGTCTGAATTACTAAAT\n++\n+BBBBAAFFFFFFGGGGGGGGGGHCDDFDGHHHHHGHHHGHHHHHHHHHHGHHHHHH\n+@SRR1203042.11 11/1\n+ATATTTCTCGTTTTTGCTCGTTAACGATAAATTAACAGTGTGCCTACAGGGCATCGTGGATGTCCATGACCTCCTCGCATACCAATAATCATTACATAC\n++\n+>AAABFFFFCBCGGGGGGGGEFGGHGFHFEGHHGHHHFHHHHHHHHHHHHGGGHHGHHGGHHHHHHHHHHHHHHHHGGGGGHGFFGHFHHHHHHHHHHG\n+@SRR1203042.12 12/1\n+CTTCACGTTCAGGCAGTTTTTTACCGCCGGCGATGACAATCGGCACCGGACAACCTGCCGCAATACGCTCAAAACCTTTATCGACATAATACGTTTTGATAATTTGCGCCCCCATTTCCGCCGCGA'..b'CGTCACTATCGATG\n++\n+CDCDCFFFFFCFGGGGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGGGGGFGGEHHHHHHHHHHHGHHHHGGGGGGGHHGGHHHHGHHH\n+@SRR1203042.990 990/1\n+GGTCTGAATAATGCTGTAACGAATACGCTCCGGCTGAGTAAACTGATCTACATGCTGGTCATAATAGGCCTGAATATCCGCATCGCTGACCGGTGCCTGCATCGTCGCGGCATCCAGCTTGATATAGCTTACGCGGAACTGTTCCGGCGTCATAAAGCGGACTTTATTCTGATCGTAGTAGCTGGACACTTCCTGAT\n++\n+BCCBCFFFFFFFGGGGGGGGGGGHGHHGGGGGGGGGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHGHHHHHHHGGGGGGGHGGHHGGGGGHHHHHHHGHHGGGGGGGHHHHHHHHHHHHHHHHHHHGGGGGGGHHHHHHGGGGGGGHHHHHHGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGFFFFF\n+@SRR1203042.991 991/1\n+GTTATTCTCATTATTTTGTTCAAAAAAAAGCCCGCTTAACAGGCGGGCCGGGTATCGTTTGGCTGATTACAGCTGTTCATACACCGCCCGCTATCAGGAAGTGCGCCACCAACCGTGTAATGCAAATGTCGCTGCCATTTTAGATACCCTCTTCATGTGAACTTTCGTACTAGTTAACTAGTTCGATGGAATAATGTCAACACCTATTTCAGTATATTTGCCGGAACCGTTATGATGTACATGACATAC\n++\n+BCBCCFFFFFFFGGGGGGGGGGHHHHGGGFHGHGGGGGHHHHHGGGGGGGGGEGFGDGHGAGHHGHHHHHHHGHHHHHHHHHHHHGGGGGGGGGHHHHHHHGGHGGGGGHHHGGGGHHHHGHHHGHHHHHHHGGGHHHHHHHHHHHHHHGGGGGGGGFFGGGGGGGGGGGGGGGGGGGGGGGGGGGFHFFFFFHFFFFHHFFFFFFFFFFFFFFFFFFFFFFFACFFFFFFFFFFFFFFFFFF0BFFFF\n+@SRR1203042.992 992/1\n+GTCATGGATTCCGTTTGCGGCTGATACAGGGTATGACACAACCAGTTGGCAT\n++\n+CCDEDFFFFFFFGGGGGGGGGGGHHHHHHHGHHHHHHHHHGGGGHHHHHHHH\n+@SRR1203042.993 993/1\n+ATATTACAGTAAATCGTTGGCTCCTGTCAGGCAACCTGGCGTTTGTATCAGTGTATTAGCCAGAATTAAATTACCGCTTTTTTAGAGCCTAATGATTCATTGTGCATCATTTTTACC\n++\n+CCDCDFFFFFFFGGGGGGGGGGHGHHHHHHHHGHHHHHHHGEGGGHHHHHHHHHHHHHHGHHHFHHHHHGHHHHHGGGGGHHGHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH\n+@SRR1203042.994 994/1\n+CCCTGATAGCGCTCGTTCATCACCCATGTGCCGTCTTTTTCCAGAAACAGTGACGTTTCAATACCTTCACAATCCGCACAGGGCAGCACGCCGCGCCAGCTTTGCTGCATGGGTTTTAAT\n++\n+CCCCDFFFFFEDGGGGGGGGGGHHHGHHHHHHGGGHGHHHHHHHHHHHHHHHHHGGGHHHHHFHHHHHHHHHHHHGGGGGHHGGGGGHHGGGGGGGGGGGHHHHHHHHHHHHGGFGGHHH\n+@SRR1203042.995 995/1\n+CTCTTGGACGCAGGAGGAATTATGGCGAAACCAGCCTATCCAACCGGCGTTGAAAACCACGGAGGTAAAC\n++\n+BCCCDFFFFCDDGGGGGGGGGGHHHHGGGGGHHHHGHHHHHHHFGGGGGGGGHHHHHGHGGGGGGEHHHH\n+@SRR1203042.996 996/1\n+CCGCTGACCACGTCAAAGTGACGGTAGCCGATGGCGCCTTCGGTGAGCGTGATCTGCACAACCGACTTAGTAGCTTCCGCCTTCTCCGGCAATTTGTTCAGATCGATACGCGCCAGGCTGCGCGAATAGCTTCCGACATCCGCAATCACGGCCTTGCCGAAAACGTTGGTTGAGGTTGGCGAGCCGCTACCGCTAACGGGGACGTCCGCAATACCGTCGGTATCAACCAGCAAACGTGTGCTGCCCGCTAA\n++\n+CDDDCCDFFFDCGGGGGGGGGGGGGHGHHGGGGGHGGGGGHHGGGGHHGGGGHHHHHHHHHGGGGGGGGHGHHHHHHHGGGGGHHHHGGGGGHHHHHHHHHHHHHGHHGGGGGGGGHHHHGGGGGGGGGHHHHHGGGGGHHGGGGGHGHGGGGGGGGGGGGGGGGGGGGFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFAFDFFFFFFFFFFFFFFFDFFFFFFFFFFFFFFFFFBEFFFFFEDFFFF\n+@SRR1203042.997 997/1\n+CACCCTGTATCGCGCGCCTTTCCAGACGCTTCCACTAACACACATGCTGATTCAGGCTCTGGGCTCCTCCCCGTTCGCTCGCCGCTACTGGGGGAATCTCGGTTGATTTCTTTTCCTCGGGGTACTTAGATGTTTCAGTTCCCCCGGTTCGCCTCATTAACCTATGGATTCAGTTAATGATAGTGTGACGAGTCACACTGGGTTTCCCCATTCGGGTATCGCCGGTTATAACGGTTCATATCACCTTACCG\n++\n+BCCDCCFFFFFDGGGGGGGGGGHHHHGGGGGGHHHHHHHHHHGGHHHHHHHHHHHHHHHHHHHHHHGHHHGGGGHHGGGHGGGGGGGGHHHHGGGGHHHHHGGGGHHHHHHHHHHHHHGGGGGGHHHHHHHHHHHHHHHHHHHHGGGGGGGGGGGHHHHGGGGGGGGGGGGGGGGGGGGGGHGGGGGGGDGGGGGFFFFFFFFEFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFAEFFFFFFFFFFFFFFD\n+@SRR1203042.998 998/1\n+TTGCAAAAGCGGACGCGCATTATCATTCCGCGCCGCCGTCGAAGCTACAGGCGGAATAACCGATATGTCCGATAGCATTATCGCCATCGGACATATTTTATCAGGCGGCGTTATACGCCTGCCTGGTCCTCTGATAAGTCCCGTACCGATTGAC\n++\n+AAAAAFFFBCA@CEAEEEGGGBHHHHHHGGEGEGEEEEGGGEEFGFDEHHGGEEG/?GHGHGECGGBFGFCGGGCH12F1FGHC?CFFGCGCCGFFDHHFH1G11GCCGGCG?GFFG?@GGGGGGEGGGGGGGBFFGGFB99AGGGGGB@F?BB\n+@SRR1203042.999 999/1\n+GGTCAACGCTGGATCAGCGATACAGAAAGCGAGCTGGGACTTGGAACCGTTGTTGCGATGGATGCGCGAACCGTCACCTTACTTTTCCCGTCCACGGGGGAAAACCGCCTGTATGCGCGCAGTGATTCTCCCGTGACCCGCGTCATGTTCAACCCTGGCGATACGATTACAAGCCATGAAGGCTGGCAGCTACATATCGATGAAGTAAAAGAAGAAAATGGCCTGCTTGTTTATGTCGGCACCCGCCTGGA\n++\n+BBBBBFFBBBBBGGGGGGGGGGGHHHHHHHGGGGGHHGFFHHHGHHHGGGGGGHHGGGHGGHHHHGGGGGGGGGGGGHHHHHHHHHFHHGHGGGHGGGGGCDHFHGGGGGHHHHGHGGGGCCDHHHHHHHHHGGGGGGGGGGGGGGGGGGGGFGGGFEFFFFFFFEFFFFFFFFFFFFFFFFEFFFFFFFFFFFFFFFFF?FBFFFFFFFFFFFFFFBFFBF/FEFFFF:BFFFFBFFFFFFF.9@CDEA.\n+@SRR1203042.1000 1000/1\n+GTGTAGGGTGACGTCATTCAAATCGGCATCGGCATATTTTTGCGATGCTTTGGGATCGAA\n++\n+BCCCCFFDFBCFGGGGGGGGGGHHGGGGGHGGGGGHHHHHHGHGGHGGHHHHHGHHGGGH\n' |
| b |
| diff -r 000000000000 -r 26df66c32861 test-data/Se-Enteritidis-refseq_masher-matches.tab --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Se-Enteritidis-refseq_masher-matches.tab Thu Feb 15 13:59:31 2018 -0500 |
| b |
| @@ -0,0 +1,2 @@ +sample top_taxonomy_name distance pvalue matching full_taxonomy taxonomic_subspecies taxonomic_species taxonomic_genus taxonomic_family taxonomic_order taxonomic_class taxonomic_phylum taxonomic_superkingdom subspecies serovar plasmid bioproject biosample taxid assembly_accession match_id +Se-Enteritidis Salmonella enterica subsp. enterica serovar Enteritidis str. CHS44 0.0 0.0 400/400 Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales; Enterobacteriaceae; Salmonella; enterica; subsp. enterica; serovar Enteritidis; str. CHS44 Salmonella enterica subsp. enterica Salmonella enterica Salmonella Enterobacteriaceae Enterobacterales Gammaproteobacteria Proteobacteria Bacteria enterica Enteritidis PRJNA185053 SAMN01041154 702979 NZ_ALFF ./rcn/refseq-NZ-702979-PRJNA185053-SAMN01041154-NZ_ALFF-.-Salmonella_enterica_subsp._enterica_serovar_Enteritidis_str._CHS44.fna |
| b |
| diff -r 000000000000 -r 26df66c32861 test-data/Se-Enteritidis.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/Se-Enteritidis.fasta Thu Feb 15 13:59:31 2018 -0500 |
| b |
| b'@@ -0,0 +1,78431 @@\n+>123_1 length_1549500_cov_48.1637\n+GCTGCTGCGTCAGCTGGTGAGCCGCGACCACACGGATATCCGGGTGTTAAGCCTGTATGC\n+GTTTAACGCCTTTGAGCAGCGGCGCTTTGGCGAGGCGGTGGCGGCCTGGGAGATGATGCT\n+GAAACTGCTGCCGGCGGGTGACGCCCGGCGGGCGGTGATAGAGCGCAGTATCCGGCTGGC\n+GCAGGAGAAATAAGACCCTGACGGCCCGGTGACGTGGCGCCATCGGGCCTGGCTTGTTAC\n+TGTATTCCGCGTGTTTGTAAAAATAGAATGGTCGCCGCGACGCGTGAGCGCACGTTTAGC\n+TTGCGAAGTAGATTACGAATGTGCACCTTAACCGTCTGCTCAGAAATATTCAGTACTGAC\n+GCAATCTGTTTGTTAGAAAGCCCCTGCGCCAGCTCATGCAAGACATCTAACTCTCGTTCG\n+GTCAGGATACTAAAGGGATCTTCCTGCGCGCCAAACCGTTCGCGCTCACGCAGATATTCA\n+TTGACCCGATCGCTAAAGACTTTACCGCCGTTAGCGCCTTTGCGAATGGCCTCCAGCAGC\n+ACTTCCGGATCGCTATCTTTGAGCAGATAACCGTCGGCGCCGGCGTCGATCAGCGCGTAG\n+ATGTCGCTGGCGGAATCCGAGACGGTAAGAATAATAATTTGCGCCGTCACACCATCCCGG\n+CGTAGCGCGTTCAGGGTATCTAACCCGCTCAGACCTTTCATATTCAGATCCAGCAGGATC\n+AGATCGGGCTCAATGCGATTCGCCAGATCGATCGCACTCGCCCCGTCACCCGCTTCGGCA\n+ACGACATGAAAAGCCGGGTCCAGTTCCAGTAATTGACGAATACCTCGCCGCATAAGTGGA\n+TGGTCGTCCACAATAAGCACCTGAAAAGGTGTTACTTCAGGCATGCTGTATCTCCTGAGT\n+TTTATTAGAATGATTATTGTTTTCAGCGCGGAAATCGTCCAGATTTGCCACATTGTCAAG\n+CGCGTAAATTTTACCCTAATTAGTGCATGGGTAAGTAGTAAAACCTGTGACAGGCGAGTA\n+ATTAGCTGAACGATAGAAAGGATAAAACAACCCGTTGTGAGAGAAAACAGAATACTCCCT\n+GAAGTTGAATACTGGTCTGGACGCTTTTTTCGGACAATGTGACATAACAGAAGTGTGGCA\n+TATGTTGCTGCGCCATTGCACCCGTAAGTCCAGACTATCTTTACTGGCAGGAAATTCCTT\n+ATTAAAAGTCATAGCGTCTAAAGCTTGTCATTATTAACAAATTATTTTAACTGAATTTAT\n+TTATGGTTTTATTAATGTCAATGAAATACATCTGAGCAGAACGAATAAACCGCGACATCT\n+GTTAAATTAAATATTAAGTCAATAGCAGAGGTATTTTTATGCGATAAAGAGATTCTGACG\n+ATATTCTTATCATAAATGAAAATGTGGTCAGGAATGAGCGTCATTCACTTATAACTTATC\n+CTGGATGTGCCTGAACAACACTCGCGGCGTTTTGAGCACCCGTTGGGGTGACTCAAGGGG\n+AGAACGTAGTGTGGATGCTATATCAGCCGTTTCTGTGAGCGTAAGCGTGGCGTAGAAAAT\n+TTTAAATATGTTAGCCGGTTAAAAATAACTATTGACATTGAAATGGTGGTGGAGTGTATA\n+TGAAGAGAATATTTATATATCTATTATTACCTTGTGCATTCGCATGTTCTGCTAATGATA\n+ATGTTTTTTTTGGCAAGGGCAACAAGCATCAGATCTCTTTTGCTGCGGGAGAAAGTATAA\n+GAAGAGGAGGGGTTGAGCACTTATATACGGCTTTTCTGACATACAGTGAACCCAGCGATT\n+TTTTCTTTTTACAGGCAAGAAATAATCTGGAGTTAGGAGGATTTAAGGCTAAGGGTAGCG\n+ATGATTGCAGTAAACATTCTGGCAGCGTTCCCTGCAATAAATATAACCAGGGCGTATTGG\n+GTATCTCGAAGGATGTGGCGCTGGTTCATTTCGCTGGTATCTATACCGGTATTGGTCTGG\n+GGGCTTATATAAAATCTAAGTCGCGAGATGATATGCGTGTCAATTCTGCATTTACCTTTG\n+GAGAAAAAGCGTTTCTTGGCTGGAACTTTGGGGCTTTTTCTACAGAAGCTTATATCCGGC\n+ATTTCTCGAATGGATCACTTACGGATAAAAATTCAGGGCATAATTTTGTAGGTGCTTCAA\n+TTAGTTATAATTTCTGAAGTTGAATAACAATTAGCGAGTTGCTGGCTGAAGGAGTAATTA\n+ATCACCGTACGTTGTCTACAAAACGTGTTGTGAATAGCCGATCGTTATCTACCCTATGGC\n+GACAGGGAGGCTAATTGTTAGTGACAAAGAAGTGGTAGGCCGTTTACCTTACCAGAACGT\n+TTTATTATTGCTGCGACAGATTGCTTACTCATTTACCTGCCACTACAAACATTTCTTCCA\n+GCATAGGGTGTAGATGCGCTTTTTCTGTTTTAGTACAAACATGGTTTACGTTATTTGCCT\n+GCATTGACTTTACGTTGACCACTGCACAGGAAAGATGTCCAATCAGTTCATGCAAAATCA\n+GTTCATGCAAAATAACGTCTCTGGCATCAGCTAACTTTTTAATTGTAGGCATAAAAAAAA\n+CCAGCCCTGACAGGCTGGTTTTCAAGGGGAATTTTGGTCGGCAGCTTCATCCGCAGCATC\n+TGCGGAGAGCAGCGCAGGTACGGCGACCACAAAAGCCGGGGAGGCATCAGCCAGCGCGGC\n+GTCGGCTGACACAGCCAGAACGGCGGCAGCCGCCTCGTCATCAGCATCGGAGGCATCCAC\n+CCACGCCGCCGCATCTGATACCAGCGCATCACTGGCAGCGCAAAGCAGAGCTGCAGCCGG\n+AGAATTGGCAACCAGAGCCGAAGAGGCCGCGAAACGGGCCGAGGATATCGCAGACGTGAT\n+TTCCCTGGAAGATGCAAGCCTGACGAAAAAAGGTATCGTTAAATTAAGCAGTGCCACGGA\n+CAGTGACAGCGAAGCGCTGGCGGCCACACCAAAGGCGGTAAAAACCGTTATGGGTGAGGT\n+ACGGACCAAAGCGCCGCTGGACAGCCCGGCATTCACTGGAACGCCGACCACACCGACGCC\n+GCCAGGCGATGCTAAAGGGCTTCAGACAACAAACGCGGAGTTTGTCCGCAAACTGATTGC\n+CGCGCTGGTTGGTTCCGTACTGGAGCCACTGGACACCCTGCAGGAACTGGCTGACGCGTT\n+GGGAAATGATCCGAACTTTGCCACCACGGTACTGAATAAACTGGCGGGCAAGCAGCCGCT\n+GGACGAAACCCTGACGGCGCTGTCAGGAAAAAGCGTTGACGGTCTTATCGAATACGTTGG\n+TTTGCGAGAAACCATAAGTCGTGCCGCCGATGCATTATAAAAATCACAGAATGGCGGCGA\n+TATTCCGGACAAGGATTTGTTTGTGCGTCGTATCGGTGCCGCGCGAGCGTTTGATGGCGC\n+AGTTACTATCGGCTGTGATGATAATCCGTGGACGACGGCGGAGTTTATCGTCTGGCTGGA\n+GTCTCAGGGCGCATTCAATCACCCTTACTGGATGTGTCGTGGCTCCTGGTCTTACGCTTA\n+TAACAAAATCATCACGGATACTGGCTGCGGTACTATCTGTCTCGCTGGCGCAGTGATTGA\n+GGTAATGGGAGTGCGTGGCGCGATGACTATTCGGGTGACAACGTCCCATTCAGTATCTGG\n+TTGGTGATACGTGGGTGACAGCCCCAAGTGTATAAGAAGGAATAATTATGACAGCGGAAA\n+AAAAATAAAAAGAACAAACAGTTTTTAAATATTAAAAATTTCATTCCGTATGCACCGGAA\n+CCAGATGACACATTATTCGCCGATGCGGCGTATCTTA'..b'h_598_cov_205.442\n+TAACCTCACAACCCGAAGATGTTTCTTTCGATTCATCATCGTGTTGCGAAAATTTGAGAG\n+ACTCACGAACAACTTTCGTTGTTCTGTGTTTCAATTTTCAGCTTGATCCAGATTTTTAAA\n+GAGCAAAACTTCGCAGTGAACCCTTTCAGGTACACTCTGAAGTATTTTTTCGTAAACACT\n+CACGAGATGGTGGAGCTATGCGGGATCGAACCGCAGACCTCCTGCGTGCAAAGCAGGCGC\n+TCTCCCAGCTGAGCTATAGCCCCATCGTGTAGTCAGAACCTCTTTACCGATAATTTTTCC\n+TGAGACAAGGCGTGGAATAACGAAGCATACATCAGTATGTGAGTTATTTCACAACGCAGT\n+ATTCAGGGAAAATTTGGTAGGCCTGAGTGGACTTGAACCACCGACCTCACCCTTATCAGG\n+GGTGCGCTCTAACCACCTGAGCTACAAGCCTGTAGAGGTTTTACTGCTCGTTTTTCATCA\n+GACAATCTGTGTGAGCACTTCAAAGAACAGTTCTTTAAGGTAAGGAGGTGATCCAACCGC\n+AGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTCATGAATCACAAAGTGGT\n+>123_25 length_531_cov_148.126\n+CACGCCCTTCATCGCCTCTGACTGCCAGGGCATCCACCGTGTACGCTTAGTCGCTTAACC\n+TCACAACCCGAAGATGTTTCTTACGATTCATCATCGTGTTGCGAAAATTTGAGAGACTCA\n+CGAACAATTTTCGTTGTTCTGTGTTTCAATTTTCAGCTTGATCCAGATTTTTAAAGAGCA\n+AATATCTCAAACGTGACTCGTAAGTCAGTTTTGAGATATTAAGGCAGGTGACTTTCACTC\n+ACAAACCAGCAAGTGGCGTCCCCTAGGGGATTCGAACCCCTGTTACCGCCGTGAAAGGGC\n+GGTGTCCTGGGCCTCTAGACGAAGGGGACGTATCAGTCTGCTTCGCAAGACGCCTTGCTA\n+TTTACTTTTCATCAGACAATCTGTGTGAGCACTGCAAAGTACGCTTCTTTAAGGTAAGGA\n+GGTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTCATGAA\n+TCACAAAGTGGTAAGCGCCCTCCCGAAGGTTAAGCTACCTACTTCTTTTGC\n+>123_26 length_492_cov_131.107\n+CACGCCCTTCATCGCCTCTGACTGCCAGGGCATCCACCGTGTACGCTTAGTCGCTTAACC\n+TCACAACCCGAAGATGTTTCTTACGATTCATCATCGTGTTGCGAAAATTTGAGAGACTCA\n+CGAACAACTTTCGTTGTTCTGTGTTTCAATTTTCAGCTTGATCCAGATTTTTAAAGAGCA\n+AATATCTCAAACGTGACTCGTAAGTCAGTTTTGAGATACTGATGGCAACGCCTTTCACAC\n+ATTACCGCGCAAGTGGCGTCCCCTAGGGGATTCGAACCCCTGTTACCGCCGTGAAAGGGC\n+GGTGTCCTGGGCCTCTAGACGAAGGGGACACTGAAGTCTCAATCGCAAGACGCCTTGCTT\n+TTTACTTTTCATCAGACAATCTGTGTGAGCACTTCAAAGAACAGTTCTTTAAGGTAAGGA\n+GGTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTCATGAA\n+TCACAAAGTGGT\n+>123_27 length_424_cov_92.2929\n+TGAAACTGGCTGAACGCATTGGGGTGGCCGCTGCCGCCCGCGAACTTAACCTGTATGAAT\n+CACAGCTCTACAACTGGCGAAGCAAACAGCAAAATCAGCTCTCTTCTTCTGAACGCGAGC\n+AGGAGATGTCCGCTGAGATCGCTCGTCTGAAACGTCAACTGGCAGAACGGGATGAGGAAC\n+TGGCCATTATCCAGAAGGCCGCGACATACTTCGCGAAGCGCCTGAAATGAAGTATGTCTT\n+CATCGAAAACCATCAGGCTGAGTTCAATATCAAAGCCATGTGCCGTGTACTTCAGATTGC\n+CCGTAGCGGCTGGTACGTCTGGCATCAGCGTCGTCATCAGATAAACCGGCGTCAGCGGTT\n+CCGCCTTGTCTGTGATAACGTCGTCCGGGAAGCATTCAGTGACGCAAAACAACGCTATGG\n+TGCG\n+>123_28 length_405_cov_70.6942\n+GGTTTCGGGTCTATACCCTGCAACTTAACGCCCAATTAAGACTCGGTTTCCCTCCGGCTC\n+CCCTATTCGGTTAACCTTGCTACAGAATATAAGTCGCTGACCCATTATACAAAAGGTACG\n+CAGTCACCCCACCCCAAAGCATTCGCTTTCGCTACGCGAAACCGCCTGCCTTTGCGCTGT\n+CGCGCAAAGCGCCCTGCGGCTCACTTTACACTGCTGTTTTATCGGTTTGACGTCGCTTCG\n+CTCCGTCAACGCGGTACAGCAAATGCTTTGGTGGTGGGGCTCCCACTGCTTGTACGTACA\n+CGGTTTCAGGTTCTTTTTCACTCCCCTCGCCGGGGTTCTTTTCGCCTTTCCCTCACGGTA\n+CTGGTTCACTATCGGTCAGTCAGGAGTATTTAGCCTTGGAGGATG\n+>123_29 length_268_cov_396.298\n+GGTTTCGGGTCTATACCCTGCAACTTAACGCCCAATTAAGACTCGGTTTCCCTCCGGCTC\n+CCCTATTCGGTTAACCTTGCTACAGAATATAAGTCGCTGACCCATTATACAAAAGGTACG\n+CAGTCACACAGGTAAACCTGTGCTCCCACTGCTTGTACGTACACGGTTTCAGGTTCTTTT\n+TCACTCCCCTCGCCGGGGTTCTTTTCGCCTTTCCCTCACGGTACTGGTTCACTATCGGTC\n+AGTCAGGAGTATTTAGCCTTGGAGGATG\n+>123_30 length_236_cov_70.5963\n+GATGCCTGGCAGTTCCCTACTCTCGCATGGGGAGACCCCACACTACCATCGGCGCTACGG\n+CGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCACCGCGCTACTGCCGCCAGGC\n+AAATTCTTTGTGCTCTGTACGCAATTCTTTATCGCATCAGCGGCGTTGCCTGCGCTCGTA\n+AACTCAGTCACATACTTCTGTATGCTCCTTCCTTTCCTTCGCTTGCCGCCTTGCTG\n+>123_31 length_166_cov_363.154\n+GCAAAAGAAGTAGGTAGCTTAACCTTCGGGAGGGCGCTTACCACTTTGTGATTCATGACT\n+GGGGTGAAGTCGTAACAAGGTAACCGTAGGGGAACCTGCGGTTGGATCACCTCCTTACCT\n+TAAAGAACTGTTCTTTGAAGTGCTCACACAGATTGTCTGATGAAAA\n+>123_32 length_151_cov_63.125\n+TGAGCCTTTTGTTTTATTTGATGTCTGGCAGTTCCCTACTCTCGCATGGGGAGACCCCAC\n+ACTACCATCGGCGCTACGGCGTTTCACTTCTGAGTTCGGCATGGGGTCAGGTGGGACCAC\n+CGCGCTAGTGCCGCCAGGCAAATTCTTTGTG\n+>123_33 length_142_cov_73.4\n+TTTGCCTGGCGGCAGTAGCGCGGTGGTCCCACCTGACCCCATGCCGAACTCAGAAGTGAA\n+ACGCCGTAGCGCCGATGGTAGTGTGGGGTCTCCCCATGCGAGAGTAGGGAACTGCCAGGC\n+ATCAAATAAAACGAAGGGCCCT\n+>123_34 length_128_cov_815\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC\n+CCCCCCCC\n' |